Statistics

Test sets

Number of protein structures: 108 CASP9 targets
Number of trials: 155520 trials = 3 (template) * 8 (alignment) * 3 (modeling) * 108 (protein) * 20 (conformation)

Success rate

Success rate for combinations of Template-searching methods.
Success rates for Alignment stage (Alignment row) and those for actual modeling processes (other rows) are tabulated separately.

HHpred PSI-blast Clustalw2 CS-blast dialign2 HHpred mafft muscle probcons t-Coffee (Fast) t-Coffee
(M-Coffee)
Alignment N.A. 104 N.A. 105 104 105 105 105 105 105
Modeller N.A. 101 N.A. 103 103 103 103 102 103 100
MR-SA N.A. 80 N.A. 80 75 80 72 79 77 79
PQR-SA N.A. 99 N.A. 103 92 99 101 89 97 89


PSI-blast PSI-blast Clustalw2 CS-blast dialign2 HHpred mafft muscle probcons t-Coffee (Fast) t-Coffee
(M-Coffee)
Alignment 68 72 N.A. 71 N.A. 71 71 71 71 73
Modeller 46 49 N.A. 50 N.A. 50 50 50 51 50
MR-SA 60 63 N.A. 68 N.A. 66 66 65 61 59
PQR-SA 64 66 N.A. 69 N.A. 68 69 67 63 61


CS-blast PSI-blast Clustalw2 CS-blast dialign2 HHpred mafft muscle probcons t-Coffee (Fast) t-Coffee
(M-Coffee)
Alignment N.A. 93 82 91 N.A. 86 86 90 94 92
Modeller N.A. 74 62 63 N.A. 62 62 59 64 60
MR-SA N.A. 68 72 74 N.A. 74 71 70 69 69
PQR-SA N.A. 78 78 83 N.A. 79 76 77 75 72



Protein-like scores for Common sets

Common sets for Template-searching methods, Alignment methods, and Modeling methods have been prepared, and protein-like scores for resulting structures are tabulated below. Note that three common sets are different each other as success rates differ.


Template-searching methods

Comparison of performances of 3 template-searching methods.


Template-searching
methods
HHpred PSI-blast CS-blast
TM-score 0.5241 0.7040 0.5844
GDT-TS 0.4660 0.6638 0.5282
RMSD 15.4699 8.6277 11.7873
DOPE -15745.0740 -18800.2762 -15895.3005
nDOPE 1.0205 -0.0342 0.8671
dDFIRE -318.6747 -377.1048 -319.9406
Clash 67.3571 29.8232 93.8142
Molprobity_RAMA 88.9041 92.9184 85.5532
Procheck_RAMA 82.5581 87.8729 78.6632
1st_packing -3.8895 -2.6956 -3.0676
2nd_packing -3.7724 -2.9423 -3.2562
Whatcheck_RAMA -0.4473 0.6975 -1.3172
Whatcheck_Rotamer 0.9862 1.2490 -0.1940
Backbone -2.0974 -1.4303 -2.4195
Length 1.0261 0.9650 1.0630
Angle 1.3561 1.2264 1.4658
Omega 1.8411 1.3641 2.1839
Planarity 2.0083 1.8565 2.4118
Improper 1.2039 1.0339 1.3519
Inside 1.1668 1.1455 1.1445



Alignment methods

Comparison of performances of total of 10 alignment methods.


Alignment methods PSI-blast Clustalw2 CS-blast dialign2 HHpred mafft muscle probcons t-Coffee (Fast) t-Coffee
(M-Coffee)
TM-score 0.7349 0.4549 0.4736 0.5315 0.2547 0.5549 0.5575 0.5602 0.5688 0.5694
GDT-TS 0.6952 0.4277 0.4560 0.4968 0.2212 0.5220 0.5251 0.5273 0.5351 0.5356
RMSD 10.2902 23.6895 12.9165 12.9292 28.1390 14.1982 15.2125 13.9442 13.0100 13.3363
DOPE -20249.8534 -13802.5172 -10802.6035 -13733.7728 -10836.0109 -15066.9162 -15005.2198 -15145.9391 -15106.6534 -15025.9789
nDOPE -0.1003 1.2596 1.1648 1.0882 2.1387 0.8039 0.8004 0.7740 0.7629 0.7686
dDFIRE -406.2954 -279.6278 -223.4138 -286.2117 -233.1739 -308.9088 -307.7021 -309.0404 -309.5063 -307.1753
Clash 34.6073 48.8026 97.0958 102.5618 85.2576 65.6124 66.2411 65.1317 64.0037 69.6006
Molprobity_RAMA 93.5770 90.1092 85.6402 86.2230 85.9261 89.6686 90.0191 89.8306 89.2156 89.5021
Procheck_RAMA 88.5466 83.9766 78.7553 79.1871 78.5639 83.6807 84.2843 83.8351 83.0392 83.2446
1st_packing -2.4865 -4.4660 -3.6025 -3.3205 -5.1202 -3.4481 -3.5477 -3.5491 -3.4582 -3.4900
2nd_packing -2.8243 -4.1410 -3.5812 -3.2841 -4.7072 -3.4802 -3.5564 -3.5599 -3.4990 -3.5326
Whatcheck_RAMA 0.7549 -0.5136 -1.3941 -1.0733 -1.7368 -0.4103 -0.3627 -0.4301 -0.5197 -0.4060
Whatcheck_Rotamer 0.9508 0.2741 -0.5766 -0.2711 -0.6390 -0.0045 0.0020 0.0192 -0.0229 0.1187
Backbone -1.2132 -1.7175 -2.6171 -2.2202 -2.3261 -1.8307 -1.7451 -1.8479 -1.8423 -1.8913
Length 0.9748 0.9979 1.0511 1.0630 1.0473 1.0119 1.0161 1.0120 1.0103 1.0164
Angle 1.2485 1.3014 1.4683 1.4521 1.4074 1.3452 1.3522 1.3403 1.3303 1.3433
Omega 1.2957 1.4602 1.9477 1.7369 1.5970 1.5024 1.4969 1.4632 1.4425 1.4646
Planarity 1.6721 1.3563 2.0218 1.7050 1.0618 1.5597 1.5569 1.5422 1.5085 1.5594
Improper 1.0566 1.0626 1.3770 1.3080 1.1651 1.1754 1.1720 1.1656 1.1547 1.1745
Inside 1.1122 1.1883 1.1415 1.1314 1.2424 1.1466 1.1458 1.1427 1.1348 1.1302

 

 

Modeling methods

Comparison of performances of 3 modeling methods.


Modeling methods Modeller MR-SA PQR-SA
TM-score 0.5113 0.5331 0.5153
GDT-TS 0.4766 0.4983 0.4738
RMSD 19.7145 17.6605 17.6450
DOPE -13724.2982 -16064.1265 -16057.0331
nDOPE 1.4208 0.7592 0.0182
dDFIRE -293.5150 -322.9149 -317.1756
Clash 126.8924 37.3048 28.4124
Molprobity_RAMA 87.0006 91.0992 91.4499
Procheck_RAMA 80.2271 85.3578 85.8231
1st_packing -3.8163 -3.6587 -3.7764
2nd_packing -3.6947 -3.5408 -3.7211
Whatcheck_RAMA -1.7292 0.2150 0.6098
Whatcheck_Rotamer -2.5757 1.8177 2.3502
Backbone -1.6219 -1.9228 -2.0469
Length 1.0817 0.9794 0.9805
Angle 1.5093 1.2689 1.2328
Omega 0.9567 1.9923 1.9238
Planarity 0.4640 2.5263 2.1135
Improper 1.3199 1.1648 1.0258
Inside 1.1050 1.1828 1.1851